Variant report

Variant	rs2579892
Chromosome Location	chr8:35380121-35380122
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10099855	0.81[ASN][1000 genomes]
rs10112860	0.80[ASN][1000 genomes]
rs10216851	0.80[ASN][1000 genomes]
rs12334629	0.80[ASN][1000 genomes]
rs12541423	0.86[CHB][hapmap]
rs12544701	0.80[ASN][1000 genomes]
rs12546786	0.85[CHB][hapmap];0.81[ASN][1000 genomes]
rs12550037	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs1439151	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1439157	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1821958	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1898829	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2243786	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2579881	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2579885	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2579886	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2579889	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2579890	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2579896	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2589333	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2589347	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2589348	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2589744	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2589749	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2589750	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2589760	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2589764	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2921109	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2921219	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35827990	0.81[ASN][1000 genomes]
rs41360948	0.81[CHB][hapmap]
rs41409549	0.81[ASN][1000 genomes]
rs6988474	0.86[CHB][hapmap];0.81[ASN][1000 genomes]
rs6991528	0.80[ASN][1000 genomes]
rs7002810	0.81[CHB][hapmap]
rs7002972	0.81[CHB][hapmap]
rs873893	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1017085	chr8:34742896-35594241	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv539546	chr8:34742896-35594241	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv520421	chr8:35155517-35479468	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1024397	chr8:35296922-35424277	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv533420	chr8:35358115-36227536	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2579892	LSM1	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:35356400-35391200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr8:35359800-35397200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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